1 RNA-Seq

1.1 Quality checks

1.1.1 Alignment statistics

1.1.2 PCC replicates

1.1.3 PCA replicates (using norm counts)

1.1.4 GFP reads (genetic system validation)

1.2 Compare GFP and noGFP systems

1.2.1 PCA between conditions (using log2FC)

1.2.2 Overlaps between up and down genes

1.3 MA plots

RNA-Seq differentially expressed genes

1.4 FC up vs down genes per cdition

1.5 Alluvial plots

Visualize transitions between conditions

1.6 Gene overlaps between conditions

1.7 Heatmap logFC genes of interest

1.8 GO up and down genes per condition

2 RNA-Seq clusters analyses

2.1 Cluster figure (heatmap, STRING network, GO, motifs)

2.2 STRING newtork per cluster

2.3 Boxplot quantif FPKM and enrichments

Stratified per cluster and PRC1 binding

2.4 Check percentage of PRC1 bound genes

2.5 Tissue specificity score

Stratified per cluster and PRC1 binding

3 CUTNRUN

3.1 Quality Checks

3.1.1 Alignment statistics

3.1.2 PCC between replicates

3.1.3 PCC between replicates

3.2 MA plots (DESeq2)

4 Reverting vs non reverting genes

4.1 Defining characteristics

4.1.1 FC between conditions

4.1.2 Overlap with RNA clusters

4.1.3 Chromhmm classes

4.1.4 Overlap with K27 and K118 domains

4.1.5 Size of overlapping K27 domains

4.1.6 FPKMs between cditions and percentile

4.1.7 GO

4.1.8 STRING network

4.1.9 Motifs enrichment

4.2 Average tracks

4.2.1 Gene promoters PH18/WT conditions

4.2.2 Gene promoters between RNAi condition

4.2.3 PH assigned peaks

PH peaks assigned to their closest gene -> split between recovery & noRecovery

4.3 Cutnrun FC between KD and PH18

4.4 K36me3 at noRecovery vs activity matched genes

5 gDNA mutations

5.1 Global overview

5.1.1 Overlaps between conditions

5.1.2 Mutation counts per condition and between conditions

5.2 Allele frequency (specific vs enriched)

5.3 Overlaps between mutations shared between several conditions

5.4 Mutations features

5.4.1 All mutations features

5.4.2 Exonic mutations features

5.5 Gene centric analysis

5.5.1 Overlapping mutant genes across conditions

5.5.2 Go of mutated genes (exonic mutations)

5.5.3 Mutations impact on FC

5.6 Mutations hotspots